Protein Structure Prediction: The Next Generation

Over the last 10-15 years a general understanding of the chemical reaction of protein folding has emerged from statistical mechanics. The lessons learned from protein folding kinetics based on energy landscape ideas have benefited protein structure prediction, in particular the development of coarse grained models. We survey results from blind structure prediction. We explore how second generation prediction energy functions can be developed by introducing information from an ensemble of previously simulated structures. This procedure relies on the assumption of a funnelled energy landscape keeping with the principle of minimal frustration. First generation simulated structures provide an improved input for associative memory energy functions in comparison to the experimental protein structures chosen on the basis of sequence alignment

Analytical and Numerical Treatment of the Mott--Hubbard Insulator in Infinite Dimensions

We calculate the density of states in the half-filled Hubbard model on a Bethe lattice with infinite connectivity. Based on our analytical results to second order in $t/U$, we propose a new `Fixed-Energy Exact Diagonalization' scheme for the numerical study of the Dynamical Mean-Field Theory. Corroborated by results from the Random Dispersion Approximation, we find that the gap opens at $U_{\rm c}=4.43 \pm 0.05$. Moreover, the density of states near the gap increases algebraically as a function of frequency with an exponent $\alpha=1/2$ in the insulating phase. We critically examine other analytical and numerical approaches and specify their merits and limitations when applied to the Mott--Hubbard insulator.Comment: 22 pages, 16 figures; minor changes (one reference added, included comparison with Falicov-Kimball model

Prolongations of Geometric Overdetermined Systems

We show that a wide class of geometrically defined overdetermined semilinear partial differential equations may be explicitly prolonged to obtain closed systems. As a consequence, in the case of linear equations we extract sharp bounds on the dimension of the solution space.Comment: 22 pages. In the second version, a comparison with the classical theory of prolongations was added. In this third version more details were added concerning our construction and especially the use of Kostant's computation of Lie algebra cohomolog

A simultaneous search for prompt radio emission associated with the short GRB 170112A using the all-sky imaging capability of the OVRO-LWA

We have conducted the most sensitive low frequency (below 100 MHz) search to date for prompt, low-frequency radio emission associated with short-duration gamma-ray bursts (GRBs), using the Owens Valley Radio Observatory Long Wavelength Array (OVRO-LWA). The OVRO-LWA's nearly full-hemisphere field-of-view ($\sim20$,$000$ square degrees) allows us to search for low-frequency (sub-$100$ MHz) counterparts for a large sample of the subset of GRB events for which prompt radio emission has been predicted. Following the detection of short GRB 170112A by Swift, we used all-sky OVRO-LWA images spanning one hour prior to and two hours following the GRB event to search for a transient source coincident with the position of GRB 170112A. We detect no transient source, with our most constraining $1\sigma$ flux density limit of $650~\text{mJy}$ for frequencies spanning $27~\text{MHz}-84~\text{MHz}$. We place constraints on a number of models predicting prompt, low-frequency radio emission accompanying short GRBs and their potential binary neutron star merger progenitors, and place an upper limit of $L_\text{radio}/L_\gamma \lesssim 7\times10^{-16}$ on the fraction of energy released in the prompt radio emission. These observations serve as a pilot effort for a program targeting a wider sample of both short and long GRBs with the OVRO-LWA, including bursts with confirmed redshift measurements which are critical to placing the most constraining limits on prompt radio emission models, as well as a program for the follow-up of gravitational wave compact binary coalescence events detected by advanced LIGO and Virgo.Comment: 14 pages, 5 figures, ApJ submitte

Architecture and Membrane Interactions of the EGF Receptor

SummaryDimerization-driven activation of the intracellular kinase domains of the epidermal growth factor receptor (EGFR) upon extracellular ligand binding is crucial to cellular pathways regulating proliferation, migration, and differentiation. Inactive EGFR can exist as both monomers and dimers, suggesting that the mechanism regulating EGFR activity may be subtle. The membrane itself may play a role but creates substantial difficulties for structural studies. Our molecular dynamics simulations of membrane-embedded EGFR suggest that, in ligand-bound dimers, the extracellular domains assume conformations favoring dimerization of the transmembrane helices near their N termini, dimerization of the juxtamembrane segments, and formation of asymmetric (active) kinase dimers. In ligand-free dimers, by holding apart the N termini of the transmembrane helices, the extracellular domains instead favor C-terminal dimerization of the transmembrane helices, juxtamembrane segment dissociation and membrane burial, and formation of symmetric (inactive) kinase dimers. Electrostatic interactions of EGFR’s intracellular module with the membrane are critical in maintaining this coupling

Insulating phases of the infinite-dimensional Hubbard model

A theory is developed for the T=0 Mott-Hubbard insulating phases of the infinite-dimensional Hubbard model at half-filling, including both the antiferromagnetic (AF) and paramagnetic (P) insulators. Local moments are introduced explicitly from the outset, enabling ready identification of the dominant low energy scales for insulating spin- flip excitations. Dynamical coupling of single-particle processes to the spin-flip excitations leads to a renormalized self-consistent description of the single-particle propagators that is shown to be asymptotically exact in strong coupling, for both the AF and P phases. For the AF case, the resultant theory is applicable over the entire U-range, and is discussed in some detail. For the P phase, we consider in particular the destruction of the Mott insulator, the resultant critical behaviour of which is found to stem inherently from proper inclusion of the spin-flip excitations.Comment: 13 pages Revtex, 12 postscript figure

Structure of the Current Sheet in the 11 July 2017 Electron Diffusion Region Event.

The structure of the current sheet along the Magnetospheric Multiscale (MMS) orbit is examined during the 11 July 2017 Electron Diffusion Region (EDR) event. The location of MMS relative to the X-line is deduced and used to obtain the spatial changes in the electron parameters. The electron velocity gradient values are used to estimate the reconnection electric field sustained by nongyrotropic pressure. It is shown that the observations are consistent with theoretical expectations for an inner EDR in 2-D reconnection. That is, the magnetic field gradient scale, where the electric field due to electron nongyrotropic pressure dominates, is comparable to the gyroscale of the thermal electrons at the edge of the inner EDR. Our approximation of the MMS observations using a steady state, quasi-2-D, tailward retreating X-line was valid only for about 1.4 s. This suggests that the inner EDR is localized; that is, electron outflow jet braking takes place within an ion inertia scale from the X-line. The existence of multiple events or current sheet processes outside the EDR may play an important role in the geometry of reconnection in the near-Earth magnetotail

The Radio Sky at Meter Wavelengths: m-Mode Analysis Imaging with the Owens Valley Long Wavelength Array

A host of new low-frequency radio telescopes seek to measure the 21-cm transition of neutral hydrogen from the early universe. These telescopes have the potential to directly probe star and galaxy formation at redshifts $20 \gtrsim z \gtrsim 7$, but are limited by the dynamic range they can achieve against foreground sources of low-frequency radio emission. Consequently, there is a growing demand for modern, high-fidelity maps of the sky at frequencies below 200 MHz for use in foreground modeling and removal. We describe a new widefield imaging technique for drift-scanning interferometers, Tikhonov-regularized $m$-mode analysis imaging. This technique constructs images of the entire sky in a single synthesis imaging step with exact treatment of widefield effects. We describe how the CLEAN algorithm can be adapted to deconvolve maps generated by $m$-mode analysis imaging. We demonstrate Tikhonov-regularized $m$-mode analysis imaging using the Owens Valley Long Wavelength Array (OVRO-LWA) by generating 8 new maps of the sky north of $\delta=-30^\circ$ with 15 arcmin angular resolution, at frequencies evenly spaced between 36.528 MHz and 73.152 MHz, and $\sim$800 mJy/beam thermal noise. These maps are a 10-fold improvement in angular resolution over existing full-sky maps at comparable frequencies, which have angular resolutions $\ge 2^\circ$. Each map is constructed exclusively from interferometric observations and does not represent the globally averaged sky brightness. Future improvements will incorporate total power radiometry, improved thermal noise, and improved angular resolution -- due to the planned expansion of the OVRO-LWA to 2.6 km baselines. These maps serve as a first step on the path to the use of more sophisticated foreground filters in 21-cm cosmology incorporating the measured angular and frequency structure of all foreground contaminants.Comment: 27 pages, 18 figure